In spite of growing evidence pointing to ecological and genetic risks to wild fish populations, artificial propagation and stocking remain common practices for recreational fishery management. Moreover, even a cursory level of monitoring and evaluation of these risks is neglected, especially where fisheries are managed by private entities. Against this backdrop and with the goal of establishing a more integrated system of ecosystem-based management, this study aims to identify potential threats from the current practices and patterns of brown trout management in Austria. We surveyed 26 private brown trout hatchery operations in three Austrian provinces to examine and categorize the practices in the production of brown trout for stocking. Specifically, we examined the rearing practices and the "trading networks" among trout farmers for characteristics such as rearing history, operating principles, broodstock origins and maintenance, and output figures. Several risk-associated practices emerged, including introduction of brood from divergent lineages outside of Austrian watersheds, translocation and mixing of fish across major watersheds within Austria, and reinforced domestication across multiple generations of captivity. These practices jeopardize native populations by disrupting local adaptations resulting from mixing of native and non-native lineages, reducing genetic diversity within lineages from population bottlenecks, and lowering success of wild populations from domestication selection within the hatchery environment. The findings, which identify threats rather than directly measure impacts, are discussed within the context of concerns on the role of conserving intraspecific diversity for native brown trout fisheries. We conclude by suggesting the integration of ecological and genetic principles into propagation and stocking practices to achieve fishery management strategies more compatible with maintaining natural diversity and adaptive potential of brown trout in Austria.